Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1228 to 1277 of 3228 in total 
Value Type: Ranked
Network Comparison Type: Divided
Interaction Map: High confidence
Filtered: 1

\def\wcA{0.16666666666667\textwidth}
\def\wcB{0.16666666666667\textwidth}
\def\wcC{0.16666666666667\textwidth}
\def\wcD{0.16666666666667\textwidth}
\def\wcE{0.16666666666667\textwidth}
\begin{longtable}{|c|c|c|c|c|}
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
description\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
red\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
green\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
network\_comparison\vspace{3pt}}\\
\hline
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
1228\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [source:swissprot;acc:p48507]\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
213.079\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
218.325\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.02462\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1229\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [source:swissprot;acc:p48506]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
1230\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
interleukin-4 induced protein 1 precursor (fig-1 protein). [source:swissprot;acc:q96rq9]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
219.55\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
214.288\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.02456\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
1231\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
212.724\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
207.637\vspace{3pt}}&\multirow{4}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.0245\vspace{3pt}}}\\\cline{1-4}
\parbox{\wcA}{\vspace{3pt}\noindent
1232\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [source:swissprot;acc:p32322]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
172.543\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
168.417\vspace{3pt}}&\\\cline{1-4}
\parbox{\wcA}{\vspace{3pt}\noindent
1233\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [source:swissprot;acc:p18669]\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
212.724\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
207.637\vspace{3pt}}}&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1234\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [source:swissprot;acc:p15259]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
1235\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin associated protein 9-4; keratin associated protein 9.4. [source:refseq;acc:nm\_033191]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
219.356\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
224.723\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.02447\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
1236\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin associated protein 4-10; keratin associated protein 4.10. [source:refseq;acc:nm\_033060]\vspace{3pt}}&\multirow{26}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
219.354\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
224.699\vspace{3pt}}}&\multirow{26}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.02437\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1237\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin associated protein 4-2; keratin associated protein 4.2. [source:refseq;acc:nm\_033062]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1238\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin associated protein 4.3 (fragment). [source:sptrembl;acc:q9byr4]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1239\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin associated protein 2-4; keratin associated protein 2.4. [source:refseq;acc:nm\_033184]\vspace{3pt}}&&&\\\cline{1-2}\cline{4-4}
\parbox{\wcA}{\vspace{3pt}\noindent
1240\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin associated protein 4-14; keratin associated protein 4.14. [source:refseq;acc:nm\_033059]\vspace{3pt}}&&\multirow{3}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
224.7\vspace{3pt}}}&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1241\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin associated protein 4.9 (fragment). [source:sptrembl;acc:q9byq8]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1242\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin associated protein 4-12; keratin associated protein 4.12. [source:refseq;acc:nm\_031854]\vspace{3pt}}&&&\\\cline{1-2}\cline{4-4}
\parbox{\wcA}{\vspace{3pt}\noindent
1243\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin associated protein 1.5. [source:refseq;acc:nm\_031957]\vspace{3pt}}&&\parbox{\wcD}{\vspace{3pt}\noindent
224.699\vspace{3pt}}&\\\cline{1-2}\cline{4-4}
\parbox{\wcA}{\vspace{3pt}\noindent
1244\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]\vspace{3pt}}&&\parbox{\wcD}{\vspace{3pt}\noindent
224.7\vspace{3pt}}&\\\cline{1-2}\cline{4-4}
\parbox{\wcA}{\vspace{3pt}\noindent
1245\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [source:swissprot;acc:o75690]\vspace{3pt}}&&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
224.699\vspace{3pt}}}&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1246\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [source:swissprot;acc:p26371]\vspace{3pt}}&&&\\\cline{1-2}\cline{4-4}
\parbox{\wcA}{\vspace{3pt}\noindent
1247\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [source:swissprot;acc:q9nsy2]\vspace{3pt}}&&\parbox{\wcD}{\vspace{3pt}\noindent
224.7\vspace{3pt}}&\\\cline{1-2}\cline{4-4}
\parbox{\wcA}{\vspace{3pt}\noindent
1248\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin associated protein 4.4. [source:refseq;acc:nm\_032524]\vspace{3pt}}&&\parbox{\wcD}{\vspace{3pt}\noindent
224.699\vspace{3pt}}&\\\cline{1-2}\cline{4-4}
\parbox{\wcA}{\vspace{3pt}\noindent
1249\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [source:swissprot;acc:q9nvd7]\vspace{3pt}}&&\multirow{7}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
224.7\vspace{3pt}}}&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1250\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [source:swissprot;acc:p48059]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1251\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [source:swissprot;acc:q13418]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1252\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [source:swissprot;acc:q96dr4]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1253\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ras suppressor protein 1 (rsu-1) (rsp-1). [source:swissprot;acc:q15404]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1254\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [source:swissprot;acc:q13283]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1255\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [source:swissprot;acc:q9un86]\vspace{3pt}}&&&\\\cline{1-2}\cline{4-4}
\parbox{\wcA}{\vspace{3pt}\noindent
1256\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin associated protein 1-3; keratin associated protein 1.3. [source:refseq;acc:nm\_030966]\vspace{3pt}}&&\parbox{\wcD}{\vspace{3pt}\noindent
224.699\vspace{3pt}}&\\\cline{1-2}\cline{4-4}
\parbox{\wcA}{\vspace{3pt}\noindent
1257\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
espin. [source:refseq;acc:nm\_031475]\vspace{3pt}}&&\multirow{5}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
224.7\vspace{3pt}}}&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1258\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [source:swissprot;acc:p10635]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1259\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [source:refseq;acc:nm\_006832]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1260\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
lim and senescent cell antigen-like domains 2; ilk-binding protein. [source:refseq;acc:nm\_017980]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1261\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
d(4) dopamine receptor (d(2c) dopamine receptor). [source:swissprot;acc:p21917]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
1262\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
keratin associated protein 9.2. [source:refseq;acc:nm\_031961]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
219.353\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
224.678\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.02428\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
1263\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [source:swissprot;acc:p53778]\vspace{3pt}}&\multirow{15}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
171.231\vspace{3pt}}}&\multirow{15}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
167.177\vspace{3pt}}}&\multirow{15}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.02425\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1264\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [source:swissprot;acc:q9nya1]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1265\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [source:swissprot;acc:q9h3h5]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1266\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [source:swissprot;acc:q96qb1]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1267\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [source:swissprot;acc:p49137]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1268\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [source:swissprot;acc:q15825]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1269\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nitrogen fixation cluster-like. [source:refseq;acc:nm\_014301]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1270\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [source:swissprot;acc:q9y3m8]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1271\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [source:swissprot;acc:q92502]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1272\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [source:swissprot;acc:q15822]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1273\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [source:refseq;acc:nm\_004635]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1274\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [source:swissprot;acc:q16539]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1275\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [source:swissprot;acc:p43681]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1276\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [source:swissprot;acc:p32297]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
1277\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [source:swissprot;acc:q9nra0]\vspace{3pt}}&&&\\\hline
nd{longtable}

Legend:
- Rank is the rank after comparing the two networks

 - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray

 - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.

 - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them

 - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.

 - Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/